Three dimensional molecular modeling software applications provide users such as chemists, pharmaceutical scientists, molecular biologists, students, and instructors with tools for viewing and manipulating three dimensional graphic representations of chemical structures. Various different types of representations of a particular chemical structure may be available for use, depending upon the individual software package. Common representations of three dimensional graphic molecular models include a ball-and-stick representation, a wire frame representation, and a space filling representation, for example. Software applications used for creating, editing, and/or viewing three dimensional molecular models include Electronic Lab Notebooks (ELN) such as E-Notebook by PerkinElmer of Waltham, Mass.; and chemistry modeling programs such as Chem3D or ChemBio3D by PerkinElmer of Waltham, Mass., and Maestro by Schrodinger of New York, N.Y. Depending upon the software application used, the file format of a three dimensional graphic molecular model may vary. For example, Chem3D and ChemBio3D use a .c3xml file format, while Maestro uses a .mae or Protein Data Bank (PDB) file format. These file formats, unlike standard image files, binary files, or computer aided design files, contain information and data fields specific to representations of molecular models.
The surface of a three dimensional (e.g., polyhedral) object may be represented in a computer aided design environment as a polygon mesh made of a collection of polygon faces of a same size and shape (e.g., triangles, quadrilaterals, etc.) that “wrap” the surface of the object. In mesh generation, adaptive meshes may be employed such that a coarse mesh is provided where there are no fine details upon the surface, and a fine mesh occurs in regions containing detailed features. Adaptive meshes, for example, save in computational requirements and disk storage requirements.
Using computer aided design data, for example, provided in STereoLithography (STL) file format developed by 3D Systems of Rock Hill, S.C. or RP format developed by the OpenRP initiative of Goa, India, a rapid prototyping machine or three dimensional printer may be used to fabricate a physical representation of a three dimensional model.
There is a need for automatic conversion of a three dimensional molecular model to standard computer aided design format to allow for immediate and user-friendly printing of a physical representation of the three dimensional molecular model.